I was thinking on different types of character advancement other than Levels. What I mean by this is a power progression or somthing of the like not directly tied to Class levels, character wealth is an example of this along with the "special" stuff our PC's get in most of our Campaigns like Nailo's Robot in Rabbi's or the elementals in Loki's. What I am looking for is something a little more substantial. Something like multiclassing but doesn't slow down class progression as much; but not nearly as strong or fast as a gestalt character.I was thinking of having these extra abilities also level up off of XP players put into them. For example a level 5 character when they kill somthing can keep their Experience or spend a portion of it on their special ability. The special ability can level up but the character level would still be 5. Similar to my fist campaign where you spent HD to strength curse marks.

Are you switching your campaign to EXP? You can't have a XP buy-in system without XP. If you do have it, the boost has to be significant to justify delaying class levels. Even then, characters with spellcaster-like mechanics still would probably be better served by avoiding it (do you want each player to enjoy benefits or is it a opt in?).

You could provide a multiclass-gestalt subsidy, as in a character can make two of their levels gestalt or take their next level. You could place limits on dipping or gestalt HD versus solo HD if you wished. Once again, this is basically a buff to characters which can benefit more from dipping. Characters which desire their latest class level (more ability/day, scaling DC, pivotal feature) will be dissuaded from the option, so if this is something you want to provide every character this may not be the method to use.

The OGC has a section on secondary classes under character advancement. Basically a character gets 3.5 feat progression instead of pathfinder and some bare-bones hallmark features of other classes. You could attempt to implement your own secondary class system, where characters are still primarily interested in their main path progression but can channel energy on a rainy day.

You could also permit a type of prestige gestalt. A lot of pathfinder prestiges are straight inferior to base classes but offer flavor. Allowing prestige classes to advance base class abilities might produce your desired effect. This probably carries the most risk of being broken like 3.5.

In Leon Nine the 'special adds' I'm doing are attached to the favor points. At certain thresholds of favor characters will get to choose between three options tailored to them and their specific favor balance. It's based on RP and exploration rather than being tied into regular character advancement.

You could do something with archetypes. You could afflict each player with a ghost that haunts them but unlocks abilities with the completion of ghost quests. As we uncover more of the lost language we can uncover abilities lost to time (some enemies can use 'em too).

We were told to start 3rd level. Not bad, not bad. So we had a fighter, a druid and a barbarian. I made a (secretly) LE human and took 1 level bard and two levels wizard (illusion). My background was sage. I said i was a teacher of a very specific subject. Whenever anyone would ask me to teach it to them or what it was i asked if they thought they were a bad guy. (usually no) i said then they didnt need to learn what i could teach.Fast forward up to level 10 and still no one knows I'm LE (His flaw is that every time my character does something evil, he fails so hard it looks good.) i havent used my bardic inspiration yet, they're wondering what or when i sing. I tell them I'm waiting for the right moment.I have 3 levels bard (college of lore) at this point and 7 levels illusionist wizard. The fighter dies and everyone is sad, but he rolls up a rogue. The rogue comes to me when the party is away and is naturally inquisitive as to what i teach and if i have a school. I say i do have a school and I ask him if he considers himself a bad person. He says when he has to be, and asks my schools name. I start singing for the first time. I manifest 3 clones of myself using major image and I say its a school to teach people how to be villians. And we are number one.